MSFragger

Using FragPipe

FragPipe can be downloaded here. Follow the instructions on that same Releases page to launch the program.

Before you get started, make sure your LC-MS file format is compatible with the workflows you want to perform (for Thermo data, we recommend converting .raw files to mzML):

Configure FragPipe

When FragPipe launches, the first tab in the window (‘Config’) will be used to configure the program.

Connect FragPipe to a MSFragger .jar program file. If you already have such a file downloaded, use the ‘Browse’ button to select it or ‘Update’ to upgrade to the latest version. If you have not downloaded MSFragger before, use the ‘Download’ button. (MSFragger installation help)

Connect FragPipe to a Philosopher program file. If you already have it downloaded, select ‘Browse’, otherwise select ‘Download’. (Philosopher installation help)

Select workflow & add spectral files

In the ‘Workflow’ tab:

Choose the workflow you want to use and press ‘Load’. A number of common workflows (including glyco) are provided, or you can customize, save and load workflows for future use (via the ‘workflows’ folder).

Drag & drop LC/MS files into the window or select ‘Add files’ or ‘Add Folder Recursively’ (to add all files in a folder, including those in subfolders). Specify the appropriate labels for the replicates/fractions in your experiment.

Notes about timsTOF data: For raw PASEF files (.d extension), each data file is a folder, so we recommend using ‘Add Folder Recursively’. If you have already run MSFragger on the .d files, make sure the .mzBIN files resulting from that analysis are in the same directory as the .d files to speed up the analysis. If you don’t need to perform quantification, .mgf or _calibrated.mgf files can be used instead of raw .d.

Once you’ve loaded your spectral files, indicate how you’d like PSM/peptide/protein reports to be generated:

For a single set of reports (search results from all input files merged)

Leave the ‘Experiment’ and ‘Replicate’ fields blank, and ensure that the ‘Multi-Experiment Report’ box on the ‘Report’ tab is not checked.

For reports with results from different fractionated replicates shown in separate columns

Indicate the ‘Experiment’ and ‘Replicate’ for each input file as shown below, where each replicate of two experimental conditions is composed of two fractions. Different fractions from the same sample should have the same ‘Experiment’/’Replicate’ name. On the ‘Report’ tab, check ‘Multi-Experiment Report’.

Path

Experiment

Replicate

run_name_1.mzML

Control

1

run_name_2.mzML

Control

1

run_name_3.mzML

Control

2

run_name_4.mzML

Control

2

run_name_5.mzML

Treatment

3

run_name_6.mzML

Treatment

3

run_name_7.mzML

Treatment

4

run_name_8.mzML

Treatment

4

Note: the ‘Replicate’ ID (e.g., 1, 2, 3, and 4 in the above table) should not be reused by different replicates from different experiments. However, if each pair of ‘Control’ and ‘Treatment’ is from the same study subject, you should use the same ‘Replicate’ ID for the corresponding ‘Control’ runs and ‘Treatment’ runs (detailed discussion can be found from https://github.com/Nesvilab/FragPipe/issues/183. We appreciate @tobiasko for the suggestion.):

Path

Experiment

Replicate

run_name_1.mzML

Control

1

run_name_2.mzML

Control

1

run_name_3.mzML

Control

2

run_name_4.mzML

Control

2

run_name_5.mzML

Treatment

1

run_name_6.mzML

Treatment

1

run_name_7.mzML

Treatment

2

run_name_8.mzML

Treatment

2

where ‘run_name_1.mzML’, ‘run_name_2.mzML’, ‘run_name_5.mzML’, and ‘run_name_6.mzML’ are controls and treatments from the same study subject; ‘run_name_3.mzML’, ‘run_name_4.mzML’, ‘run_name_7.mzML’, and ‘run_name_8.mzML’ are controls and treatments from another study subject.

Note: for compatibility with the Resource for Evaluation of Protein Interaction Networks (REPRINT), ‘Experiment’ names should be written as follows:

Negative controls: CONTROL_1, CONTROL_2, CONTROL_3, etc.

Bait IPs: [GENE]_[replicate], where [GENE] is the official gene symbol of the protein, e.g. HDAC5_1. If there are multiple conditions for the same bait protein (e.g. mutant and wt), use HDAC5_wt_1 and HDAC5_mutant_1 format.

Specify a protein sequence database

If you haven’t made a database file using FragPipe/Philosopher before, select ‘Download’ to fetch one from Uniprot. Specify the download location, then choose your options and select an organism (use the uniprot proteome ID to specify your own, e.g. ‘UP000000625’ for E. coli).

Use ‘Browse’ to select a FASTA file from a previous FragPipe/Philosopher analysis.

If you need to use a custom FASTA database, it must follow a certain format and contain decoy sequences. Click ‘Browse’ to navigate to your custom FASTA. If you select ‘Try Auto-Detect’, 50% of the entries should contain the decoy tag. For help adding decoys and database formatting, see the instructions on the ‘Database’ tab or here.

Set MSFragger search parameters

In the ‘MSFragger’ tab, check that the search parameters are suitable for your analysis. You can choose to save a customized parameter file to load for future use, or save the entire workflow (from either the ‘Workflow’ or the ‘Run’ tab).

Note: For non-specific searches or for searches with many variable modifications, you may need to use the database splitting option, which requires an installation of Python.

Validation

If you previously updated the downstream parameters when setting MSFragger search parameters, you can skip to the next section. You can also load default downstream processing parameters by selecting the appropriate ‘Load defaults’ button. In most cases, search results from MSFragger must be filtered by PeptideProphet and ProteinProphet.

For open search workflows, select Crystal-C to remove open search artifacts and improve the interpretability of your results.

Quantification

To perform quantification, make sure Label-Free Quantification and/or Isobaric Labeling-Based Quantification are selected in their respective tabs (note that workflows can be performed without any quantification, in which case spectral counts will be reported).

For label-free quantification, a match-between-runs (MBR) option through IonQuant can be turned on for closed search workflows.

For label-based quantification,

Select a labeling reagent.

For each experiment as set in the ‘Workflow’ tab, select ‘Edit/Create’ Sample/Channel Annotation to assign sample information to each TMT/iTRAQ channel.

In the annotation pop-up window:

Load the selected TMT/iTRAQ channels.

Provide the experiment/replicate information for each channel.

PTMs

For open search-based workflows, PTM-Shepherd summarizes delta masses and provides reports on residue localization, retention time similarity, and more.

Spectral library generation

Spectral libraries can be generated within closed search-based workflows. A library will be generated for each experiment specified in the ‘Workflow’ tab. Experiments must contain more than one spectral file.

Run FragPipe

Browse for the folder where you would like the search results to be written.

Press ‘RUN’ to begin the analysis! See the MSFragger wiki, FAQ, and previous questions on Github for more help.